Angels Of The Black Flag
by This-Pen-Name-Is-Too-Long
Summary: When Mary Winchester dies under unusual circumstances aboard the HMS Lawrence, John Winchester develops an intense hatred for pirates. So when John's youngest son Sam is taken by the Yellow-eyed Pirate, it will be up to Sam's older brother Dean, to rescue him, with the help of the strange Captain Novak. Pirates of the Caribbean AU


_*Aboard the HMS Lawrence*_

The moon sat low above the water, her pale beams reflecting off the gently lapping waves. The water gently rocked the body of the HMS Lawrence as the ship sat anchored in the vast ocean. On board, all was quiet. The noise of dinner had died down as all those not needed for night watch had made their way to the crew cabin. The only remaining sound was the gentle slap of waves breaking against the Lawrence, and the deep, almost calming groans of the ship as it rocked. Mary Winchester lay calmly in the cabin she shared with her husband John. For some reason, she was having trouble sleeping, but was content to lay on the bed, listening to the soothing lullaby of the ship. Having been aboard it for so long with her family, on their way to her newly promoted husband's post in Sioux Falls, the Lawrence had become almost a second home to the Winchesters, and the movement of the anchored ship had done wonders in sending baby Sammy off to sleep. At the thought of her baby, Mary rose from the bed and wrapped herself in a robe, taken over by the urge to check on the younger of her two sons. Little Sam was barely half a year old now, but had already proven to be a smart child. His eyes would lock onto yours, and you were struck with the intelligence in those hazel orbs. And Dean was growing up so fast. He was already four years old now, and was growing into such a protective big brother, Mary couldn't be prouder.

With thoughts of the two boys on her mind, Mary made her way into the cabin next to hers and John's, where Sam and Dean had been staying while at sea. Standing in the doorway, she had a brief flash of fear as her eyes adjusted and she noticed the figure standing beside Sam's crib, their back to her. "John, is that you?" She whispered, breathing a sigh of relief when her husband nods in reply, back still facing her. She held a hand to her heart as she calmed herself, reassured that it was just her husband checking on their son on his way back to the cabin. She smiled, watching John settle Sam, the fussy baby feeding from a bottle. A quick glance around the small cabin showed Mary that her older son was not in his bed, which had unfortunately become a habit for the curious toddler. There was many a night when the Lawrence's watchman had escorted the young Winchester back to his room after a late night visit to the ship deck. Mary quietly slipped away, intent on finding Dean and sending him back to bed. She just hoped he hadn't been out too long, the weather was getting cooler and it wouldn't do for the young boy to get sick.

The sea breeze brought goosebumps to Mary's arms as she reached the deck, the wooden boards cool against her bare feet. For a moment, she stood still at the top of the steps, just looking out at the vast ocean that seemed to go on forever, soft waves illuminated by the luminous moon. What a sight it was. _Now I can understand why John loves his job so much,_ Mary though to herself. _If I could see this almost every night, I don't know how I could leave the sea._

She took a deep breath, inhaling as much salty sea air as she could, before exhaling and making her way fully onto deck, eyes searching for her eldest child. What she saw sent such a deep wave of fear and shock through her, she stumbled. There, further up deck and lit up by the light of gas lanterns, was Dean, sound asleep in the arms of a man, who was in the middle of conversation with the ship's Captain. That was not what scared Mary. What scared her was who it was holding the sleeping child. That was her husband. There he stood, clutching their dozing child in one arm, the other patting the Captain on the back. _So,_ Mary though, dread filling her as each second passed, _who is in Sam's room?_

Immediately she turns and runs, fear stealing any though of calling out, only one idea going through her head. _Get to Sam_. Although it feels like much longer, it is barely a minute before Mary is back outside the doorway to her sons' room. Rushing in, she knocks the mysterious figure away from Sam, causing the feeding bottle to crash to the ground, where it shattered, spilling its contents onto the hardwood floor. The stranger shoved at Mary, pushing her to the ground beside the broken bottle, her hands stinging as small shards of glass dig into her skin. Mary catches her breath, looking down at the spilled liquid, feeling the already heavy ball of alarm grow as she notices the bottle was filled with something that looked eerily like…blood. Her observation is interrupted when she is yanked back to her feet by a hand on her throat. Struggling to breathe, Mary is dimly aware of Sam crying in his bed as she stares into the unnaturally yellow eyes that seemed to glow in the darkness. As her vision grows dark, Mary can only send a prayer out for her baby. _Please God._ She begs, heart thundering in her chest as her lungs scream for air. _Please let my baby be safe. Let him live._

* * *

John Winchester's arm aches from the weight of his son, who sits curled against his father's chest, face turned into John's neck. Despite the pain, John can't help but smile down at Dean. The boy looks so serene in his sleep, face smooth and care free. He reminds John of Mary, from the blonde hair to his soft eyelashes. John brushed the four year old's hair back from his face, full of peace from the gentle huffs of breath against his neck, coupled with the lapping of water against the ship's hull. He knows he should take Dean back to bed and out of the open air, but he is reluctant to break the moment. So he continues to stare out at the water, breathing in the salt and sea. In the midst of his relaxation, John can hear a faint sound, almost unnoticeable. He smiles when he recognizes the crying of a baby. So, little Sammy is awake. John turns away from the ocean, making his way down to the sleeping quarters. If Sam is awake, then Mary will be there in a heartbeat to soothe the upset child, and no doubt she will notice that Dean is missing from his bed. If she were to find out that John didn't take Dean straight back to his cabin after finding his wandering on deck, the John will be in big trouble.

As he gets closer to Sam's cries, Dean begins to stir, roused from sleep by his brother's distress. John hushes the mumbling toddler, assuring him that the both of them will go and check on the baby. Dean calms down when they arrive outside the shared room. With a quick glance, John notices that Mary is not in the room, so quickly steps into the next room, expecting to find her deep asleep in bed. When that turned out not to be the case, John was confused. Mary hadn't made a habit of wandering the ship at night, but perhaps she was looking around for John. With that idea in mind, John gently placed Dean down on his own two feet, ruffling the boy's hair as the tired child rubbed at his eyes with clenched fists.

After a quick search, John located one of the lanterns from his room, lighting it with a quick strike of a match. The yellow glow lit up the room. John picked up the light source, taking Dean's hand in the other and walking back towards the other room. He froze in the doorway.

Directly across from him, his wife stood against the far wall, her white nightclothes stained bright red, blood still dripping from the wound in her stomach. He eyes were blank as they stared at John, blood dripping from the corners like tears. In front of her, Sam was still crying in his cot, mouth stained by something dark and red. John's stance was broken as he gave a cry of despair, walking into the room towards his prone wife. In the back of his mind, he could hear Dean calling to him, his tone filled with confusion and fear, but that came second to Mary. He had to get to Mary, to hold her, staunch the bleeding and bring her back around. He had to. John could not lose his wife, he just couldn't. However, he was snapped from his almost trance-like state by a bright flare of orange fire as it sprouted from Mary's stomach, growing until it completely engulfed her and the wall she had been standing against. John brought his arms up to protect his face from the wave of heat. He locked on to Sam, whose quieting cries had been reborn into screams of terror. Running forward, John scooped Sam into his arms, before depositing him into the smaller arms of Dean, who was looking back at John, expression petrified.

"Take your brother up to deck and into a lifeboat as fast as you can!" John ordered his son, raising his voice in order to be heard over the crackling fire. "Alert the night watch on deck, tell him there's a fire and to get everyone off the ship." He spun Dean around, pushing him out the doorway. "Now Dean, go!

* * *

Dean ran through the Lawrence as fast as he could with his short legs, gripping tightly to his baby brother, terrified of the very thought of dropping Sam. His chest was heaving after sprinting up the steps, his head whipping this way and that in search of the man on watch. There. Dashing as fast as possible, Dean ran over to the man.

"There's a fire." Dean gasped, head light from the combination of adrenaline and lack of oxygen. "Dad says you hafta' get everyone into lifeboats!"

The watchman's face is serious as shouts and screams begin to float up onto the deck, ship passengers being awoken by the roaring flames and crackling wood. He quickly ushers Dean to the nearest longboat as more people run up the deck stairs towards the boats. Dean is hefted into the boat with Sam, later joined by a mixture of men and women. There is no sight of his dad, but Dean doesn't cry. His dad was always telling him he needed to be brave for Sammy, that his little brother would be looking up to Dean to teach him how big boys acted. So Dean would be a big boy, and would hold in the tears that threatened to spill, for Sammy. As his longboat was lowered into the water, the sounds of chaos on deck grew. The warning bell became to toll, alerting any that were not already aware of the danger, while women screamed for safety, clamouring for a place on a longboat. As the passengers in Dean's boat watched the Lawrence go up in flames, Dean looked down at his little brother. Sammy had stopped crying now, and lay calmly in Dean's arms, staring up at his big brother. Dean sniffled, smiling back and reaching with one arm to grab one of Sam's tiny hands, smile growing stronger when the little fingers grip back. As Dean watches his brother, he notices Sam's eyes drift off to the side, locking on to something. Following his gaze, Dean is shocked to notice another ship. Off to the left of the burning Lawrence, another ship sails into the distance, partially hidden in a dense fog Dean was sure had not been there earlier. There is a large flag fluttering atop the mast, pitch black but for the white Jolly Roger.

 _Pirate!_ Dean thinks in confusion. _How had pirates gotten so close to the Lawrence without anyone noticing?_

Dean's view of the ship is temporarily blocked by a large dark shape that fell from the ship, landing in the water beside the longboat with a loud splash. A few seconds later, the head of John Winchester breaks the surface of the water, his face grim and streaked with soot that the brief contact with water had not washed off. As John began swimming to the boat's side, Dean feels a wave of relief wash over him. His dad had made it out, although…

Mary Winchester is nowhere to be seen. Dean had seen her in his and Sam's room, against the wall, but only a glimpse of her. Then there had been fire, and his Dad pushing him from the room. If Mary had still been in the room when the fire erupted…

The tears finally break free, dripping down his face and off the tip of his nose. His Mom was gone. How did this even happen? There hadn't been any source of fire in the room until his dad had taken in the lantern. It just didn't make sense. Unless… Dean turns back to the stretch of ocean the unknown pirate ship had been sailing on, but he is shocked to see it is gone. Not even the fastest ship the fleet his father was a part of was fast enough to have disappeared from view in such a short amount of time. There was no sign of the hulking black ship, with its tattered flag, and strangely enough even the fog had completely dissipated, leaving empty water. Dean could only stare blankly at the place he had seen the pirates, as his father pulled himself aboard the longboat and shuffled closer to his sons. He was sure there had been something there, the fastest ship in the ocean, likely long gone by now. Dean hoped that was the last time he would ever see that boat.

Unfortunately, it was not.

* * *

 _This is hopefully going to be a regularly updated fic. I already have several pages of planning done for future chapters so, fingers crossed. Thanks for reading. If you have any criticism, please feel free to express it._

 _Until next time,_

 _-Penn_


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